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High-Throughput Sequence Analysis

The exhaustive list of topics in High-Throughput Sequence Analysis Problems in which we provide Help with Homework Assignment and Help with Project is as follows: 

  • Work with Large Multi-Entry Text Files
    • BioIndexedFile Object
    • Source File
  • Manage Short-Read Sequence Data in Objects
    • Sequence Alignments
    • BioMap Object
    • Coverage of a Reference Sequence                                                                                    
    • Filter Read Sequences Using SAM Flags                                                               
    • Sequence and Quality Data in a BioRead                                                               
    • Alignment/Mapping
  • Store and Manage Feature Annotations in Objects
    • Annotation Object                                                                           
    • Feature Annotations in a GFFAnnotation
    • Feature Annotations with Short-Read Sequence                                                                                
  • Visualize and Investigate Short-Read Alignments
    • Alignments of Multiple Data Sets                                                                                    
    • NGS Browser                                                                                   
    • Reference Sequence                                                                                
    • Feature Annotations                                                                                  
    • Insertions and Deletions                                                                           
    • Location, Quality Scores, and Mapping                                                                          
    • Pileup View of Short Reads                                                                                 
    • Specific Region of the Alignment            
  • Identifying Differentially Expressed Genes from
  • RNA-Seq Data
  • Exploring Protein-DNA Binding Sites from Paired-End
  • ChIP-Seq Data
  • Exploring Genome-wide Differences in DNA
  • Methylation Profiles